Genes, Alleles and Genomes

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What is a gene?

Johannsen (1909) - 'unit of inheritance'

Darwin (1868) - 'pangenesis'

De Vries (1900) - 'pangen'

Garrod (1908) - 'inborn errors of metabolism'

- unit of inheritance dictated production of proteins

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Beadle and Tatum (1941)

Experiments with Neurospora crassa

Why Neurospora crassa?

  • the wild type can synthesise all necessary amino acids (grows on minimal media: sugars, salts and biotin)
  • haploid life style
  • forms haploid spores or fuses, meiosis and formation of haploid sexual spores
  • it is smaland has a short generation time

The N. crassa wild type was treated with UV/X rays and then grown on a complete media. Mutants which were unable to synthesise 1 amino acid were then isolated to perform sexual crosses.

This leads to 1 gene ==> 1 enzyme. It is then extended to 1 gene ==> 1 protein and then finally 1 gene ==> 1 polypeptide.

Pauling: haemoglobin is a multimeric protein (a2b2)

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Genetic information

How dows the gene encode the necessary information for a polypeptide?

  • Crick (1958)
  • Watson and Crick's model assumed that the gene are colinear with the proteins that they code for.
  • i.e. sequence of nucleotides correlates directly with the sequence of amino acids

Experiments with bp insertions into DNA

  • Yanofsky et al
    • E.coli; tryptophan synthetase gene
  • Brenner et al
    • T4 phage
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Reading Codons

Niremberg and Matthaei (1961)

Three bases = CODON

UUU = Phe

UUUUUU = Phe-Phe (dipeptide)

AAA = Lys

CCC = Pro

GGG = Nothing

1966: all codons assigned to the genetic code

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Features of the genetic code

  • degenerate
  • 20 amino acids
  • 64 codons
  • 61 code for amino acids
  • Val: has more than one codon (synonymous codons)
  • Met: only one codon
  • All mRNA start translation with AUG. (initiation codon)
  • If methionine is not required as the first amino acid in the finished protein, it is cleaved off.
  • All mRNA stop translation with a termination codon: UAG (amber), UAA (ochre), UGA (opal)
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Translation and transcriptional signals

  • Genomes are much bigger than the transcript (mRNA)
  • Transcripts are much longer than the protein encoding sequences
  • The movement of information from mRNA (nucleotides) to polypeptides (amino acids) travels from 5' to 3'
  • Open reading frame (ORF) = AUG initiation codon
  • Movement continues until a termination codon is reached in the same reading frame
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Point Mutations

If you change a base pair for another then...

  • nothing happens - silent (degenerate genetic code)
  • change one amino acid for another - missense
  • generate a stop codon - nonsense

If you add/delete a base pair then...

  • FRAME SHIFT MUTATIONS

Where do point mutations occur?

  • translation signals embedded within transcribed sequence
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Gene

Gene

  • DNA sequence
  • Codes for a functional RNA
  • Transcribed spaces
  • Introns and exons
  • Control sequences

Gene Activity

  • No transcription

OR

  • Transcription
    • Rate of transcription
    • Pattern of transcription
    • All cells or some?
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Specialised function genes

E.coli enzymes needed to metabolise a specific C source that might not be always available

- lac; lactose metabolism

Differentiation in eukaryotes

- liver cell vs. muscle cell vs. brain cell

Eukaryotic mRNA genes may be, but need not be, interrupted:

Introns:

  • have to be spliced out prior to transport out of the nucleus for translation in the cytoplasm
  • genes are discontinuous not dispersed
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Why bother?

  • The exons are discrete protein domains
    • haemoglobin, immuniglobin, several enzymes
  • Shuffle exons between different genes and get new genes
  • Chance of chiasmata occurring increases with distance
    • So increases variability at meiosis
  • Chiasmata would occur within introns rather exons
    • less chance of disruption of protein encoding part of gene
  • Can also get more than 1 type of protein from a single gene
    • For example:
    • alpha-amylase
      • liver and silvary gland
    • Calcitonin/Calcitonin gene related protein
      • thyroid and brain
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Prokaryotes

E.coli - 4.6 x 10^6 bp DNA 

1897 known protein encoding genes

21 rRNA transcription units

84 tRNA genes

397 ORF

Single copies of each of the 1897 + 397 genes = 2294 unique sequences

Accounts for 80% of the genome as gene sequences

i.e. coding for a functional RNA molecule

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Jacob and Monod (1961)

Lactose utilisation in E.coli

Lac operon:

Regulatory gene (I) - Control sites (P)(O) - Structural genes (Z)(Y)(A)

Operator (O): regulatory sequence

Promoter (P): point of attachment for RNA polymerase

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Viral Genomes

Only able to package a set amount of DNA in the particle

Some (all?) metabolic functions off loaded onto the host cell

There are some proteins that are virus specific and are not coded for by the host cell

Viruses

  • NOT small cells
  • NOT semi-autonomous self replicating units
  • Obligate parasites
  • Use host machinery
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OX174

OX174

  • One of the smallest of bacteriophages
  • 5400nt and 9 necessary proteins
  • If 1 amino acid needs 3nt to code for it, 10-15% more DNA is required

Sanger et al, 1977

  • Completely sequenced the genome
  • Different reading frames
  • Overlapping genes, 1 gene embedded within another
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Eukaryotes

  • Time constraints during the cell cycle are less than that for E.coli
  • Larger genome
  • Different cell types
  • Different stages in the life cycle
  • Existance of mitochondria and chloroplasts

Homo sapiens genome: 3.3 x 10^9 bp (haploid)

  • Some genes are haploid genome/appear once
  • Some are identical multicopy gene families
  • rRNA, tRNA, 5S rRNA, histones
  • Simple gene families
  • Identical members arranged tandemly
  • Gene product needed in large amounts
  • Some genes have several versions: alleles (poymorphic loci)
  • Duplication of genes
    • Complex gene families
    • Related to each other but has its own specific functions e.g alpha/beta globins
    • Members expressed at different stages: embryo-foetus-adult
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H. sapiens

Gene number

20 - 25,000 pol II genes - introns + exons + gene related sequences = 30% DNA (10% exon)

+ 467 tRNA genes

+ 97 snoRNA

+ 280 rRNA 

+ 2,000 5S rRNA

+ the rest of the RNA types

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